1. Course: Analyzing Next-Generation Sequencing Data (2011 version)

    The second iteration of our bioinformatics summer course, Analyzing Next-Generation Sequencing Data, just finished. It was a great success, at least judging from the comments that people made to us personally; the evaluations aren't yet complete.

    The what: a two week course on analyzing next-gen sequencing data, using the Amazon …

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  2. Trying out 'cram'

    I desperately need something to run and test things at the command line, both for course documentation (think "doctest" but with shell prompts) and for script testing (as part of scientific pipelines). At the 2011 testing-in-python BoF, Augie showed us cram, which is the mercurial project's internal test code ripped …

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  3. My new data analysis pipeline code

    First, I write a recipe file, 'metagenome.recipe', laying out my job description for, say, sequence trimming and assembly with Velvet:

    fasta_file soil-data.fa
    
    qc_filter min_length=50 remove_Ns=true
    
    graph_filter min_length=400
    
    velvet_assemble k=33 min_length=1000 scaffolding=True
    

    Then I specify machine parameters, e.g. 'bigmem.conf':

    [defaults]
    n_threads …
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